Mercurial > repos > iuc > ncbi_eutils_elink

comparison elink.py @ 0:59063d2e91c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:40:20 -0400
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children 2791c731fc65
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-1:000000000000 0:59063d2e91c6
1 #!/usr/bin/env python
2 import argparse
3 import json
4
5 import eutils
6
7
8 if __name__ == '__main__':
9 parser = argparse.ArgumentParser(description='EFetch', epilog='')
10 parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
11 parser.add_argument('dbfrom', help='Database containing input UIDs')
12 parser.add_argument('cmd', choices=['neighbor', 'neighbor_score',
13 'neighbor_history', 'acheck', 'ncheck', 'lcheck',
14 'llinks', 'llinkslib', 'prlinks'],
15 help='ELink command mode')
16 # Only used in case of neighbor_history
17 parser.add_argument('--history_out', type=argparse.FileType('w'),
18 help='Output history file', default='-')
19
20 parser.add_argument('--user_email', help="User email")
21 parser.add_argument('--admin_email', help="Admin email")
22 # ID Sources
23 parser.add_argument('--id_list', help='list of ids')
24 parser.add_argument('--id', help='Comma separated individual IDs')
25 parser.add_argument('--history_file', help='Fetch results from previous query')
26
27 # TODO: dates, linkname, term, holding
28 # neighbor or neighbor_history and dbfrom is pubmed
29 # parser.add_argument('--datetype', help='Date type')
30 # parser.add_argument('--reldate', help='In past N days')
31 # parser.add_argument('--mindate', help='Minimum date')
32 # parser.add_argument('--maxdate', help='maximum date')
33
34 # Output
35 args = parser.parse_args()
36
37 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
38 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
39
40 payload = {
41 'dbfrom': args.dbfrom,
42 'cmd': args.cmd,
43 }
44 if args.history_file is not None:
45 payload.update(c.get_history())
46 else:
47 payload['id'] = ','.join(merged_ids)
48
49 # DB can be 'none' in a few cases.
50 if args.db != "none":
51 payload['db'] = args.db
52
53 results = c.link(**payload)
54
55 if args.cmd == "neighbor_history":
56 history = c.extract_history(results)
57 args.history_out.write(json.dumps(history, indent=4))
58
59 print results